Three-Point-Star Deoxyribonucleic Acid Tiles with the Core Arm Length at Three Half-Turns for Two-Dimensional Archimedean Tilings and Beyond

2D Archimedean tiling and complex tessellation patterns assembled from soft materials including modular DNA tiles have attracted great interest because of their specific structures and potential applications in nanofabrication, nanoelectronics, nanophotonics, biomedical sensing, drug delivery, therapeutics, etc. Traditional three- and four-point-star DNA tiles with the core arm length at two half-turns (specified as three- and four-point-star-E previously and abbreviated as 3PSE and 4PSE tiles here) have been applied to assemble intricate tessellations through tuning the size of inserted nT (n = 1-7, T is thymine) loops on helper strands at the tile center. Following our recent findings using a new type of four-point-star tiles with the core arm length at three half-turns (specified as four-point-star-O previously and abbreviated as 4PSO tiles here) to assemble DNA tubes and flat 2D arrays, we report here the cross-hybridization weaving architectures at the tile center to construct three new 3PSO tiles with circular DNA oligonucleotides of 96-nt (nucleotides) serving as the scaffolds, further the monotonous and combinatory E- and O-tilings on one type of 3PSO tiles to create 2D Archimedean tiling patterns (6.6.6) and (4.8.8), and finally, the combination of 3PSO with 4PSO as well as 2PSO tiles to tile into complex tessellation patterns. The easy realization of regular and intricate DNA tessellations with 2-4PSO tiles not only richens the fundamental DNA modules and complex DNA nanostructures in types but also broadens the potential application scopes of DNA nanostructures in nanofabrication, DNA computing, biomedicine, etc.

Structural Description of Chiral E-Tiling DNA Nanotubes with the Chiral Indices (n,m) and Handedness Defined by Microscopic Imaging

In structural DNA nanotechnology, E-tiling DNA nanotubes are evidenced to be homogeneous in diameter and thus have great potential in biomedical applications such as cellular transport and communication, transmembrane ion/molecule channeling, and drug delivery. However, a precise structural description of chiral DNA nanotubes with chiral parameters was lacking, thus greatly hindering their application breadth and depth, until we recently raised and partly solved this problem. In this perspective, we summarize recent progress in defining the chiral indices and handedness of E-tiling DNA nanotubes by microscopic imaging, especially atomic force microscopy (AFM) imaging. Such a detailed understanding of the chiral structures of E-tiling DNA nanotubes will be very helpful in the future, on the one hand for engineering DNA nanostructures precisely, and, on the other, for realizing specific physicochemical properties and biological functions successfully.

Construction of DNA Bilayer Tiles and Arrays Using Circular DNA Molecules as Scaffolds

Using oligonucleotides to weave 2D tiles such as double crossovers (DX) and multi-arm junction (mAJ) tiles and arrays is well-known, but weaving 3D tiles is rare. Here, we report the construction of two new bilayer tiles in high yield using small circular 84mer oligonucleotides as scaffolds. Further, we designed five E-tiling approaches to construct porous nanotubes of microns long in medium yield via solution assembly and densely covered planar microscale arrays via surface-mediated assembly.

Rapid Signal Amplification Based on Planetary Cross-Catalytic Hairpin Assembly Reactions

Non-enzymatic nucleic acid catalytic systems based on branch migration have been developed, with applications ranging from biological sensing to molecular computation. A scalable planetary cross-catalytic (PCC) system is built up in this work by cross-cascading three planetary catalytic hairpin assembly (CHA) reactions with a central three-arm-branched CHA reaction. With the bottom-up hierarchy strategy, we designed four levels of catalytic reactions, simple CHA reactions, two-layered linear cascades, conventional one-planetary PCC reactions, and two- and three-planetary PCC reactions, and examined the reaction products and intermediates in each level via native polyacrylamide gel electrophoresis. The gel shift assay optimized the designs of hairpin strands to keep the leaking reactions at a manageable level and protect against signal attenuation during serial signal transduction in nucleic acid circuits. The reaction kinetics, measured via fluorescence, are strongly dependent on the number of planetary reactions. As a result, the three-planetary PCC system achieved an exponential amplification factor of about 3^k, while the conventional one-planetary cross-catalytic system has an amplification factor of 2^k (k represents the cycling number). Finally, we demonstrated the rapid detection of a cancer biomarker, microRNA141, used as the catalyst in a two-planetary PCC system. We envision that the PCC systems could be applied in biological signal transduction, biocomputing, rapid detection of single- and multi-target nucleic acid probes, etc.

Tuning the Roundabout of Four-Point-Star Tiles with the Core Arm Length of Three Half-Turns for 2D DNA Arrays

By rationally adjusting the weaving modes of point-star tiles, the curvature inherent in the tiles can be changed, and various DNA nanostructures can be assembled, such as planar wireframe meshes, perforated wireframe tubes, and curved wireframe polyhedra. Based on the weaving and tiling architectures for traditional point-star tiles with the core arm length at two DNA half-turns, we improved the weaving modes of our newly reported four-point-star tiles with the core arm length at three half-turns to adjust their curvature and rigidity for assembling 2D arrays of DNA grids and tubes. Following our previous terms and methods to analyze the structural details of E-tiling tubes, we used the chiral indices (n,m) to describe the most abundant tube of typical assemblies; especially, we applied both one-locus and/or dual-locus biotin/streptavidin (SA) labelling strategies to define the configurations of two specific tubes, along with the absolute conformations of their component tiles. Such structural details of the DNA tubes composed of tiles with addressable concave and convex faces and packing directions should help us understand their physio-chemical and biological properties, and therefore promote their applications in drug delivery, biocatalysis, biomedicine, etc.

Regulation of 2D DNA Nanostructures by the Coupling of Intrinsic Tile Curvature and Arm Twist

The overwinding and underwinding of DNA duplexes between junctions have been used in designing left- and right-handed DNA origami nanostructures, respectively. For DNA tubes obtained from self-assembled tiles, only a theoretical approach of the intrinsic curvature of the tiles has been previously used to explain their formation. Details regarding the quantitative and structural descriptions of the tile's intrinsic curvature in DNA nanostructures have so far never been addressed. In this work, we designed three types of tile cores built around a circular scaffold using three- and four-branched junctions. Joining the tile cores with arms having two kinds of inter-tile distances, an odd and an even number of DNA half-turns, tended to form planar 2D lattices and tubes, respectively. Streptavidin bound to biotin was used as a labeling technique to characterize the inside and outside surfaces of the tubes and thereby the tile conformation of dihedrals with addressable faces. DNA tubes with either right- or left-handed chirality were obtained by the coupling of the intrinsic curvature of the tiles with the arm twist. We were able to assign the chiral indices (n,m) to a tube with its structure resolved by AFM at the single-tile level and therefore to estimate the global curvature of the tube (or its component tile) using a regular polygon model that approximated its transverse section. A deeper understanding of the integrated actions of different types of twisting forces on DNA tubes will be extremely helpful in engineering more elaborate DNA nanostructures in the future.

Two-layer stacked multi-arm junction tiles and nanostructures assembled with small circular DNA molecules serving as scaffolds

One-layer multi-arm junction (mAJ) motifs have been investigated extensively for many kinds of planar 2D (two-dimension) lattices, surface-curved 3D (three-dimension) polyhedra, and complex 3D wireframe and tensegrity structures. Herein, we report the weaving strategy to achieve two-layer stacked multi-arm junction tiles (abbreviated as mAJ²) of 3AJ² and 4AJ², and several primary tessellation nanostructures of nanocages and 2D rhombus lattices carrying beautifully embossed 4-point stars. Challenges for perfect tessellation are also raised regarding the increase of motif complexity from 2D to 3D.

Small Circular DNA Molecules as Triangular Scaffolds for the Growth of 3D Single Crystals

DNA is a very useful molecule for the programmed self-assembly of 3D (three dimension) nanoscale structures. The organised 3D DNA assemblies and crystals enable scientists to conduct studies for many applications such as enzymatic catalysis, biological immune analysis and photoactivity. The first self-assembled 3D DNA single crystal was reported by Seeman and his colleagues, based on a rigid triangle tile with the tile side length of two turns. Till today, successful designs of 3D single crystals by means of programmed self-assembly are countable, and still remain as the most challenging task in DNA nanotechnology, due to the highly constrained conditions for rigid tiles and precise packing. We reported here the use of small circular DNA molecules instead of linear ones as the core triangle scaffold to grow 3D single crystals. Several crystallisation parameters were screened, DNA concentration, incubation time, water-vapour exchange speed, and pH of the sampling buffer. Several kinds of DNA single crystals with different morphologies were achieved in macroscale. The crystals can provide internal porosities for hosting guest molecules of Cy3 and Cy5 labelled triplex-forming oligonucleotides (TFOs). Success of small circular DNA molecules in self-assembling 3D single crystals encourages their use in DNA nanotechnology regarding the advantage of rigidity, stability, and flexibility of circular tiles.

2D DNA lattice arrays assembled from DNA dumbbell tiles using poly(A-T)-rich stems

Poly(A-T)-rich sequences have been applied as stems of DNA dumbbell tiles for construction of single crystalline 2D DNA lattice arrays in slightly acidic solutions. These arrays show much higher stability and better organised crystalline lattice structures than those assembled from DNA dumbbell tiles with randomly sequenced stems in slightly alkaline environments. DNA nanotechnology probably provides a useful platform to study the mechanical properties of DNA duplexes with specific sequences.

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

This article presents a detailed protocol for synthesis of small circular DNA molecules, annealing of circular DNA motifs, and construction of 1D and 2D DNA nanostructures. Over decades, the rapid development of DNA nanotechnology is attributed to the use of linear DNAs as the source materials. For example, the DAO (double crossover, antiparallel, odd half-turns) tile is well-known as a building block for construction of 2D DNA lattices; the core structure of DAO is made from two linear single-stranded (ss) oligonucleotides, like two ropes making a right hand granny knot. Herein, a new type of DNA tiles called cDAO (coupled DAO) are built using a small circular ss-DNA of c64nt or c84nt (circular 64 or 84 nucleotides) as the scaffold strand and several linear ss-DNAs as the staple strands. Perfect 1D and 2D nanostructures are assembled from cDAO tiles: infinite nanowires, nanospirals, nanotubes, nanoribbons; and finite nano-rectangles. Detailed protocols are described: 1) preparation by T4 ligase and purification by denaturing PAGE (polyacrylamide gel electrophoresis) of small circular oligonucleotides, 2) annealing of stable circular tiles, followed by native PAGE analysis, 3) assembling of infinite 1D nanowires, nanorings, nanospirals, infinite 2D lattices of nanotubes and nanoribbons, and finite 2D nano-rectangles, followed by AFM (Atomic Force Microscopy) imaging. The method is simple, robust, and affordable for most labs.

DNA dumbbell tiles with uneven widths for 2D arrays

DNA dumbbell tiles of A_O(E) and B_O(E), with stem spans of 11 and 16 bp twisting two head loop motifs of each tile into parallel and antiparallel conformations respectively, were constructed to grow planar nanoribbon arrays and nanotubes as well.

Construction of a Holliday Junction in Small Circular DNA Molecules for Stable Motifs and Two-Dimensional Lattices

Design rules for DNA nanotechnology have been mostly learnt from using linear single-stranded (ss) DNA as the source material. For example, the core structure of a typical DAO (double crossover, antiparallel, odd half-turns) tile for assembling 2D lattices is constructed from only two linear ss-oligonucleotide scaffold strands, similar to two ropes making a square knot. Herein, a new type of coupled DAO (cDAO) tile and 2D lattices of small circular ss-oligonucleotides as scaffold strands and linear ss-oligonucleotides as staple strands are reported. A cDAO tile of cDAO-c64nt (c64nt: circular 64 nucleotides), shaped as a solid parallelogram, is constructed with a Holliday junction (HJ) at the center and two HJs at both poles of a c64nt; similarly, cDAO-c84nt, shaped as a crossed quadrilateral composed of two congruent triangles, is formed with a HJ at the center and four three-way junctions at the corners of a c84nt. Perfect 2D lattices were assembled from cDAO tiles: infinite nanostructures of nanoribbons, nanotubes, and nanorings, and finite nanostructures. The structural relationship between the visible lattices imaged by AFM and the corresponding invisible secondary and tertiary molecular structures of HJs, inclination angle of hydrogen bonds against the double-helix axis, and the chirality of the tile can be interpreted very well. This work could shed new light on DNA nanotechnology with unique circular tiles.

A whole genome sequence association study for puberty in a large Duroc × Erhualian F2 population

A large proportion of gilts and sows are culled from reproduction populations because of anestrus and pubertal reproductive failure. Selecting early onset of puberty gilts has a favorable effect on sows' reproductivity. However, age at puberty is hard to be routinely measured in commercial herds. With molecular genetic predictors, identifying individuals that have a propensity for early onset of puberty can be simplified. We previously performed genome scanning and a genome-wide association study for puberty in an F2 resource population using 183 microsatellites and 62 125 SNPs respectively. The detection power and resolution of identified quantitative trait loci were very low. Herein, we re-sequenced 19 founders of the F2 resource population in high coverage, and whole genome sequences of F2 individuals were imputed to perform an association study for reproductive traits. A total of 2339 SNPs associated with pubertal reproductive failure were identified in the region of 30.94-40.74 Mb on SSC7, with the top one, positioned at 33.36 Mb, explaining 16% of the phenotypic variances. We improved the magnitude of the P-value by 10E+5 to 10E+7 using the whole genome sequence rather than using low/middle density markers as in previous studies, and we narrowed down the QTL confidence interval to 5.25 Mb. Combining the annotation of gene function, RAB23 and BAK1 were perceived as the most compelling candidate genes. The identified loci may be useful in culling sows failing to show estrus by marker-assisted selection to increase reproductive efficiency of swine herds.

DNA nanotubes assembled from tensegrity triangle tiles with circular DNA scaffolds

Using small circular DNA molecules of different lengths as scaffolds, we successfully synthesised DNA nanotubes consisting of Mao's DNA tensegrity triangle tiles with four-arm junctions (Holliday junctions) at all vertices. Due to the intrinsic curvature of the triangle tile and the consecutive tile alignment, the 2D arrays are organised in the form of nanotubes. Two sized triangle tiles with equilateral side lengths of 1.5 and 2.5 full helical turns are connected by the sticky ended cohesion of a duplex with a length of 2.5 helical turns respectively, and their parallel lozenge tiling lattices were demonstrated by high resolution AFM images, where the former lozenge unit cell has a lattice constant of 13.6 nm, and the latter has a larger lattice constant of 17.0 nm. Modification of the triangle tile with infinitesimal disturbance on side lengths and insertion of one thymine single stranded loop at every vertex resulted in comparably similar nanotubes.

Assembling RNA Nanoparticles

RNA nanoparticles are designed and self-assembled according to noncanonical interactions of naturally conserved RNA motifs and/or canonical Watson-Crick base-pairing interactions, which have potential applications in gene therapy and nanomedicine. These artificially engineered nanoparticles are mainly synthesized from in vitro transcribed RNAs, purified by denaturing and native polyacrylamide gel electrophoresis (PAGE), and characterized with native PAGE, AFM, and TEM technologies. The protocols of in vitro transcription, denaturing and native PAGE, and RNA nanoparticle self-assembly are described in detail.

2D DNA lattices constructed from two-tile DAE-O systems possessing circular central strands

We reported a classical two-tile system of DAE-O (doublecrossover, antiparallel, and even half-turns tiles with odd half-turns connection) to construct regular single crystalline 2D (two dimensional) DNA lattices, using pre-circularised oligonucleotides of 42-, 64-, and 84-nt (nucleotides) as the central looped strands in DAE tiles respectively. DAE tiles with 42- and 64-nt as central strands, either in circular form or in linear form, grew regular single crystalline lattices well. However DAE tiles including a circular 84-nt as the central strand grew single crystalline lattices, those including a linear 84-nt as the central strand grew polycrystalline 2D lattices. A subtle difference in the lateral rigidity of DAE tiles with regard to the duplex axis was suggested to be the cause of the morphological difference.

SUSCEPTIBILITY LOCI FOR UMBILICAL HERNIA IN SWINE DETECTED BY GENOME-WIDE ASSOCIATION

Umbilical hernia (UH) is a complex disorder caused by both genetic and environmental factors. UH brings animal welfare problems and severe economic loss to the pig industry. Until now, the genetic basis of UH is poorly understood. The high-density 60K porcine SNP array enables the rapid application of genome-wide association study (GWAS) to identify genetic loci for phenotypic traits at genome wide scale in pigs. The objective of this research was to identify susceptibility loci for swine umbilical hernia using the GWAS approach. We genotyped 478 piglets from 142 families representing three Western commercial breeds with the Illumina PorcineSNP60 BeadChip. Then significant SNPs were detected by GWAS using ROADTRIPS (Robust Association-Detection Test for Related Individuals with Population Substructure) software base on a Bonferroni corrected threshold (P = 1.67E-06) or suggestive threshold (P = 3.34E-05) and false discovery rate (FDR = 0.05). After quality control, 29,924 qualified SNPs and 472 piglets were used for GWAS. Two suggestive loci predisposing to pig UH were identified at 44.25MB on SSC2 (rs81358018, P = 3.34E-06, FDR = 0.049933) and at 45.90MB on SSC17 (rs81479278, P = 3.30E-06, FDR = 0.049933) in Duroc population, respectively. And no SNP was detected to be associated with pig UH at significant level in neither Landrace nor Large White population. Furthermore, we carried out a meta-analysis in the combined pure-breed population containing all the 472 piglets. rs81479278 (P = 1.16E-06, FDR = 0.022475) was identified to associate with pig UH at genome-wide significant level. SRC was characterized as plausible candidate gene for susceptibility to pig UH according to its genomic position and biological functions. To our knowledge, this study gives the first description of GWAS identifying susceptibility loci for umbilical hernia in pigs. Our findings provide deeper insights to the genetic architecture of umbilical hernia in pigs.

Genome-wide association study identifies QTLs for EBV of backfat thickness and average daily gain in Duroc pigs

Backfat thickness (BFT) and average daily gain (ADG) are two important economic traits in commercial swine production. Identifying QTLs and uncovering the molecular mechanism for BFT and ADG would greatly help to speed up the breeding progress. In current breeding program, EBV for these two traits are calculated and formulated a comprehensive breeding index, which then be used to improve pig performance. Using Illumina PorcineSNP60 BeadChip, a pilot genomewide association studies (GWAS) for BFT and ADG in 83 Duroc pigs were performed. A total of 31 genome-wise significant SN Ps were detected to be associated with BFT on SSC 4, 9, 11, 12 and 14, ten of which were coincident with previously reported QTL regions. There are two genome-wise loci prominently associated with ADG on SSC2 and SSC13, respectively. The two loci on SSC2 are well overlapped with the QTL regions previously reported. All the 31 significant SNPs associated with BFT are verified on 219 outbreed pigs, six SN Ps reach an extreme significant level and seven SNP reaches a significant level, CACNA1E and ACBD6 are chosen as positional candidate genes. Our findings not only confirmed previously findings, but also revealed a number of novel SNPs associated with BFT and ADG. Two positional candidate genes CACNA1E and ACBD6 were identified for further study. These results would facilitate the identification of causative genes for BFT and ADG.

Light-driven reversible strand displacement using glycerol azobenzene inserted DNA

Tethered with bistable 2′,6′-dimethylazobenzene via a glycerol linker, an artificial 35 nt-long DNA has performed photoresponsive hybridization and reversible light-driven strand displacement.

EDC/NHS activation mechanism of polymethacrylic acid: anhydride versus NHS-ester

Both stable intermediates of anhydride and NHS-ester were observed after EDC/NHS activation of PMAA, where NHS-ester waxes, while anhydride wanes complementarily with increasing fragmentation degree of PMAA blocks in PMAA-associated polymer blends.

Small circular DNA molecules act as rigid motifs to build DNA nanotubes

Small circular DNA molecules with designed lengths, for example 64 and 96 nucleotides (nt), after hybridization with a few 32-nt staple strands respectively, can act as rigid motifs for the construction of DNA nanotubes with excellent uniformity in ring diameter. Unlike most native DNA nanotubes, which consist of longitudinal double helices, nanotubes assembled from circular DNAs are constructed from lateral double helices. Of the five types of DNA nanotubes designed here, four are built by alternating two different rings of the same ring size, while one is composed of all the same 96-nt rings. Nanotubes constructed from the same 96-nt rings are 10-100 times shorter than those constructed from two different 96-nt rings, because there are fewer hinge joints on the rings.

RCA strands as scaffolds to create nanoscale shapes by a few staple strands

Thousands of nucleotide(nt)-long single strand DNAs, generated from rolling-circle-amplification (RCA), were used as scaffolds to create DNA nanoscale wires and plates with a few short staple strands by following the origami design principle with a crossover at 1.5 turns. The core sequence of the circle template, for producing tens and hundreds of tandemly repeated copies of it by RCA, was designed according to Seeman's sequence design principle for nucleic acid structural engineering (Seeman, N. C. J. Biomol. Struct. Dyn. 1990, 8, 573). The significance for folding the RCA products into nanoscale shapes lies in the design flexibility of both staple and scaffold strand codes, simplicity of a few short staple strands to fold the periodic sequence of RCA products, and lower cost.

Different EDC/NHS activation mechanisms between PAA and PMAA brushes and the following amidation reactions

Infrared spectroscopy was applied to investigate the well-known EDC/NHS (N-ethyl-N'-(3-(dimethylamino)propyl)carbodiimide/N-hydroxysuccinimide) activation details of poly(acrylic acid) (PAA) and poly(methacrylic acid) (PMAA) brushes grafted on porous silicon. Succinimidyl ester (NHS-ester) is generally believed to be the dominant intermediate product, conveniently used to immobilize biomolecules containing free primary amino groups via amide linkage. To our surprise, the infrared spectral details revealed that the EDC/NHS activation of PMAA generated anhydride (estimated at around 76% yield and 70% composition), but not NHS-ester (around 5% yield and 11% composition) under the well-documented reaction conditions, as the predominant intermediate product. In contrast, EDC/NHS activation of PAA still follows the general rule, i.e., the expected NHS-ester is the dominant intermediate product (around 45% yield and 57% composition), anhydride the side product (40% yield and 28% composition), under the optimum reaction conditions. The following amidation on PAA-based NHS-esters with a model amine-containing compound, L-leucine methyl ester, generated approximately 70% amides and 30% carboxylates. In contrast, amidation of PAA- or PMAA-based anhydrides with L-leucine methyl ester only produced less than 30% amides but more than 70% carboxylates. The above reaction yields and percentage compositions were estimated by fitting the carbonyl stretching region with 5 possible species, NHS-ester, anhydride, N-acylurea, unreacted acid, unhydrolyzed tert-butyl ester, and using the Beer-Lambert law. The different surface chemistry mechanisms will bring significant effects on the performance of surface chemistry-derived devices such as biochips, biosensors, and biomaterials.

A proximity-based programmable DNA nanoscale assembly line

Our ability to synthesize nanometer-scale particles with desired shapes and compositions offers the exciting prospect of generating new functional materials and devices by combining the particles in a controlled fashion into larger structures. Self-assembly can achieve this task efficiently, but may be subject to thermodynamic and kinetic limitations: Reactants, intermediates and products may collide with each other throughout the assembly timecourse to produce non-target instead of target species. An alternative approach to nanoscale assembly uses information-containing molecules such as DNA1 to control interactions and thereby minimize unwanted crosstalk between different components. In principle, this method should allow the stepwise and programmed construction of target products by fastening individually selected nanoscale components – much as an automobile is built on an assembly line. Here, we demonstrate that a nanoscale assembly line can indeed be realized by the judicious combination of three known DNA-based modules: a DNA origami2 tile that provides a framework and track for the assembly process, cassettes containing three distinct two-state DNA machines that serve as programmable cargo-donating devices3,4 and are attached4,5 in series to the tile, and a DNA walker that can move on the track from device to device and collect cargo. As the walker traverses the pathway prescribed by the origami tile track, it encounters sequentially the three DNA devices that can be independently switched between an ‘ON’ state allowing its cargo to be transferred to the walker, and an ‘OFF’ state where no transfer occurs. We use three different types of gold nanoparticles as cargo and show that the experimental system does indeed allow the controlled fabrication of the eight different products that can be obtained with three two-state devices.

Click-chemistry-conjugated oligo-angiomax in the two-dimensional DNA lattice and its interaction with thrombin

The recently arising antithrombin drug, angiomax, was successfully conjugated with a 5'-amino oligonucleotide through click chemistry. This oligo-angiomax conjugate was assembled into a two-dimensional DNA lattice with other oligonucleotides together. Besides the plane sheet of DNA lattices, an interesting angiomax-involved DNA tubing structure, constructed by 40 to 50 angiomax stripes which are parallel to the longitudinal axis of the tube, was also imaged. After incubation of thrombins with the angiomax-involved DNA lattice, the binding of thrombins to arrayed angiomax peptides was observed. Finally a chromogenic substrate bioassay was employed to estimate the antithrombin activities as assembled oligo-angiomax DNA lattice approximately 1.1, oligo-angiomax approximately 2.7 angiomax. The functionalized DNA lattices have the potential to be used as a powerful platform for investigation of biomolecular interactions such as drug-protein, protein-protein, DNA-RNA, and DNA-protein interactions in the nano- and subnanoscales.

A genome-wide scan reveals candidate susceptibility loci for pig hernias in an intercross between White Duroc and Erhualian

Pig scrotal/inguinal and umbilical hernias are the most prevalent congenital disorders in pigs and often cause animal welfare problems and economic loss. To identify susceptibility loci for these traits, a genome-wide scan with 194 microsatellite markers covering the pig genome was performed in a White Duroc x Erhualian resource population with 23 scrotal/inguinal F(2) animals, 50 umbilical F(2) animals, and their unaffected siblings. A sex-average linkage map with a total length of 2,350.3 cM and an average marker interval of 12.84 cM was constructed. Both nonparametric genome-wide linkage (NPL) analysis and transmission disequilibrium test (TDT) were implemented to detect closely linked markers. The NPL analysis revealed 11 chromosomal regions on SSC1, 2, 3, 6, 7, 8, 10, and 11 for umbilical hernia and 5 regions on SSC2, 4, 8, 13, and 16 for scrotal/inguinal hernia, whereas the TDT test identified susceptibility loci for umbilical hernia on SSC1, 2, 4, 7, 10, 13, 14, and 15 and for scrotal/inguinal hernias on SSC2, 8, 10, and 18. The most promising loci were SWR1928 on SSC7 and SW830 on SSC10 for umbilical hernia, and SW933 on SSC8 for scrotal hernia, which were consistently detected by both NPL and TDT. Several previously reported chromosomal regions for scrotal/inguinal hernia were confirmed, and new evidence for linkage with this pig defect was found. Moreover, susceptibility loci for pig umbilical hernia were detected for the first time.

Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate

The aim of nanotechnology is to put specific atomic and molecular species where we want them, when we want them there. Achieving such dynamic and functional control could lead to programmable chemical synthesis and nanoscale systems that are responsive to their environments. Structural DNA nanotechnology offers a powerful route to this goal by combining stable branched DNA motifs with cohesive ends to produce programmed nanomechanical devices and fixed or modified patterned lattices. Here, we demonstrate a dynamic form of patterning in which a pattern component is captured between two independently programmed DNA devices. A simple and robust error-correction protocol has been developed that yields programmed targets in all cases. This capture system can lead to dynamic control either on patterns or on programmed elements; this capability enables computation or a change of structural state as a function of information in the surroundings of the system.

Gel-pad microarrays templated by patterned porous silicon for dual-mode detection of proteins

A proof-of-concept study demonstrated the feasibility of a novel gel-pad microarray on porous silicon chips, by initiation of an atom transfer radical propagation (ATRP) polymerisation of (polyethylene glycol) methacrylate (PEGMA) with surface Si-H species, stepwise chemical conversions of the gel membrane to an NTA-Ni2+/histidine-tagged protein system, and matrix-assisted laser desorption/ionisation mass spectroscopy (MALDI MS) and fluorescence detections.

AFM and multiple transmission-reflection infrared spectroscopy (MTR-IR) studies on formation of air-stable supported lipid bilayers

Supported lipid bilayers (SLBs) were prepared by deposition of unilamellar vesicles on a silicon substrate. Atomic force microscopy (AFM) and a new Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR) developed by us were used to trace the dynamic formation of lipid bilayers on the silicon surfaces. The evolution from deformation of vesicles to formation of bilayers can be distinguished clearly by AFM imaging. MTR-IR provided high quality infrared spectra of ultrathin lipid bilayers with high sensitivity and high signal to noise ratio (SNR). The structural and orientational changes during vesicle's fusion were monitored with MTR-IR. MTR-IR shows superiority over other infrared approaches for ultrathin films on standard silicon wafers in view of its economy and high sensitivity. Both MTR-IR and AFM results were consistent with each other and they provided more information for understanding the self-assembling procedure of SLBs.

Metal Acetylacetonate Domains Grown on H-Terminated Porous Silicon at Room Temperature and Their Specific I−V Behavior

Porous silicon (PS) was incubated in an organic solution of metal acetylacetonates of Mn(acac)(3), Fe(acac)(3), Co(acac)(3), and Ni(acac)(2) (acac = MeCOCHCOMe) at room temperature. Crystal-like domains were found to be spontaneously self-assembled on PS surfaces by atomic force microscopy (AFM). Spectroscopic studies with attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and X-ray photoelectron spectroscopy (XPS) revealed that the domains were grown from metal acetylacetonates. Current sensing atomic force microscopy (CSAFM) was used to measure the I-V curves of domains in nanoscale and specific step-jump currents on the manganese and cobalt acetylacetonate domains were surprisingly detected.

Surface reactions of 4-aminothiophenol with heterobifunctional crosslinkers bearing both succinimidyl ester and maleimide for biomolecular immobilization

Surface reactions of 4-aminothiophenol (4-ATP) with a series of heterogeneous crosslinkers containing both maleimide and succinimidyl ester groups were investigated with infrared reflection absorption spectroscopy (IRRAS) and X-ray photoelectron spectroscopy (XPS). Two types of surface reactions exist: (1) for most crosslinkers, a dominant reaction of amine and succinimidyl ester gave homogeneous maleimide-pendant surfaces; (2) for other crosslinkers, a side reaction between amine and maleimide, accompanying the main reaction, yielded heterogeneous surfaces with two linking groups, maleimide and succinimidyl ester. A typical example for the second case is the reaction of surface amines with N-succinimidyl-6-maleimidylhexanoate (SMH). Finally, a peptide, H-Gly-Arg-Gly-Asp-Ser-Pro-Cys-OH (GRGDSPC), was immobilized on the SMH-derived surface as a bridging structure through two linkages, cysteine thioether and glycine amide.

Grazing Angle Mirror-Backed Reflection (GMBR) for Infrared Analysis of Monolayers on Silicon

An easy handling infrared measurement, grazing angle mirror-backed reflection (GMBR), has been established to analyze the silicon-based organic monolayer. Theoretical prediction gave the optimal configuration with p-polarized irradiation near a grazing angle 78.1 degrees of incidence. Experimental measurement of hydrogen-terminated, undecylenic acid (UA) and N-hydroxysuccinimide (NHS) functionalized silicon (111) surfaces showed good signal peaks and reproducibility.